According to Poole and Penny, there has been far too much speculation about the origin of eukaryotes. "The conflicting hypotheses currently on offer show a curious disregard for mechanism." Up until the mid-1990s, the 'archezoa hypothesis' was dominant. "This maintained that a protoeukaryote (with nucleus) engulfed the mitochondrial ancestor". Support for the theory came from archezoa: anaerobic eukaryotes with no mitochondria, suggesting that "eukaryotes began diversifying before mitochondria entered the picture". The authors point out that this hypothesis has two independent components: "(a) that a protoeukaryote host (PEH) engulfed the mitochondrial ancestor, and (b) that modern archezoa are 'missing links' that never possessed mitochondria."
Hypothesis (b) "is now universally rejected" and the evidence is that the archezoa are derived, not missing links. The authors continue: "Hypothesis (a) was also rejected, and because eukaryotes and archaea share a number of similar genes, the deposed PEH was replaced with archaea. Consequently, incorporation of the mitochondrion - not the origin of the nucleus - was hailed as the defining event in eukaryotic origins. This opened the floodgates of speculation, and numerous new hypotheses emerged. None is supoported by observation: no archaea reside within bacteria, viruses have preposterously few similarities to the nucleus, and no RNA cells exist." The authors go on to develop their critique of these newer hypotheses and to defend the PEH theory. They argue that a nucleus-bearing protoeukaryote was the direct ancestor of modern eukaryotes.
The comments about "floodgates of speculation" in the name of science are undoubtedly correct. They apply generally to the Darwinian story-telling tradition, in which scientists propose speculative scenarios rather than document the real problems that should constrain thinking. Poole and Penny have provided us with a welcome caution about the way science should be done, but have they really gone further than acknowledging the problems? Their ancestral host is a protoeukaryote, not something else! This is the problem of irreducible complexity (noted previously here and here) and it is not going to go away!
Engulfed by speculation
Anthony Poole & David Penny
Nature 447, 913 (21 June 2007) | doi:10.1038/447913a
Abstract: The notion that eukaryotes evolved via a merger of cells from the other two domains - archaea and bacteria - overlooks known processes.
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